A NOVEL PLATFORM FOR TAXONOMIC AND FUNCTIONAL PROFILING OF THE GUT MICROBIOME

Abstract

The advent of metagenomic approaches revolutionized our understanding of the role of gut microbial communities and their interactions with the host. However, due to the dominant perception that the majority of bacteria are unculturable, their functional and phenotypic characteristics remain unknown. To address this problem, we developed a novel platform for high-throughput specific phenotypic selection of environmental microbial strains and communities. We collected samples from gastrointestinal tract of the herbivorous fish Kyphosus sydneyanus, which is a hindgut fermenter. Applying the two main approaches, 16S ribosomal RNA gene amplicons and shotgun metagenomics, we profiled the taxonomic composition and functional diversity of the microbial species and compared the ones presented in the original samples to those that grew in the lab. A total of 96 strains were isolated, representing 52 novel species from 10 families belonging to the phyla Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria In addition, of the 52 species cultured, 47 were strict anaerobes. The metabolic analysis also revealed that the variance in dietary algae, may influence the gut microbiota, due to the difference in nutritional composition between algal groups. In conclusion, our approach enables not only the large-scale culturing and phenotyping of novel microbial species but also unlocks the fish intestinal microbiota for metabolic capabilities. The potential application of seaweed degrading microbes for fishmeal protein production will be discussed. Acknowledgements : New Zealand Government Funding